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spatial expression data and H&E images alignment #3

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wwYinYin opened this issue Dec 14, 2024 · 1 comment
Open

spatial expression data and H&E images alignment #3

wwYinYin opened this issue Dec 14, 2024 · 1 comment

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@wwYinYin
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Excellent work. The article says “the spatial expression data and H&E images were aligned in a semi-manual process to honor their serial nature and allow efficient comparison as well as transfer of histopathological annotations from the H&E images.” Could you please share the alignment code? Or provide the aligned data? Thank you very much.

@jklughammer
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Hi, the anndata objects available on scp and cellxgene already contain the aligned coordinates/HE images. If you use the provided coordinates of data and HEs of the same sample to plot in the same space you will see that they are aligned.
Beyond that the code used to aid the alignment can be found here:

def aligner(adatas,img_idx,registration,dat_idxs,img_idx2=None,figsize=(12,12),dot_sizes=4.5,he_method="HE_highres",adjust=False,change=False,adjust_HE=True):

And here you can follow the individual alignment process of each sample: HTAPP_MBC/03_spatial_analysis/00.1_processing

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